Z. F. Brotzakis

AlphaFold Prediction of Structural Ensembles of Disordered Proteins

This paper shows that AlphaFold can predict structural ensembles for disordered proteins by using inter-residue distances.

Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments

This study uses MEMMI to analyze the transient interactions between the fuzzy coat and cross-β core of Aβ42 filaments, revealing differences in solubility between familial and sporadic AD forms.

Multiplexed Digital Characterisation of Misfolded Protein Oligomers via Solid-State Nanopores

This paper introduces a single-molecule method using solid-state nanopores and DNA barcoding to detect and characterize misfolded protein oligomers, demonstrating its application to α-synuclein in Parkinson's disease.

Structure-based discovery of small molecule inhibitors of the autocatalytic proliferation of alpha-synuclein aggregates

This study identifies small molecules that inhibit alpha-synuclein aggregate proliferation using structure-based and kinetic assays.

Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

The paper develops MEMMI, a cryo-EM method that determines structure and dynamics of large systems, and applies it to study the fuzzy coat of an IAPP amyloid fibril.

Discovery of Potent Inhibitors of α-Synuclein Aggregation Using Structure-Based Iterative Learning

This paper uses structure-based machine learning to identify potent small molecule inhibitors of α-synuclein aggregation, achieving compounds two orders of magnitude more potent than previous reports.

Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes

This study investigates protein aggregation in SARS-CoV and SARS-CoV-2 proteomes, finding that several SARS-CoV-2 proteins form cytotoxic aggregates via a nucleation-dependent mechanism.

A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms

The paper determines the structural ensemble of a tau-microtubule complex using cryo-EM, revealing phosphorylation and acetylation sites that destabilize the complex.

Accelerating the Calculation of Protein-Ligand Binding Free Energy and residence Times using Dynamically Optimized Collective Variables

This study predicts ligand binding modes and computes binding free energy and unbinding rates using a novel combination of computational methods, revealing water and solvation as dominant slow degrees of freedom.

Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables

The paper uses a variational approach to metadynamics to study conformational transitions in L99A T4 Lysozyme, identifying two intermediate states with reduced computational cost.